This invention was made with support from the National Institutes of Health under grant number R01/AI23909 and the United States government has certain rights in the invention.
1. Field of the Invention
The invention relates to the creation, interconversion and use of libraries of polyclonal antibodies, cell surface receptors and other proteins with variable regions. These variable regions are linked, cloned into expression vectors which can be maintained, selected and amplified as desired, and the libraries or sub-libraries of variable regions transferred to other expression vectors without loss of overall diversity or complexity. The resulting libraries of variable regions and libraries of whole proteins can be used to treat, prevent or diagnose specific diseases and disorders including neoplasias, malignancies, infections, and genetics defects and deficiencies.
2. Description of the Background
Lymphocytes constitute about 20% of blood leukocytes and are the main components of the mammalian antigen recognition system occurring predominantly in two forms, B cells and T cells. T cells differentiate in the thymus, and possibly other tissues, into cytotoxic (Tc) cells, helper (TH) cells and suppressor (Ts) cells. These T cells recognize foreign antigen in association with major histocompatibility complex (MHC) antigens via a specific T cell receptor (TcR). This receptor is highly polymorphic and clonally distributed. The typical TcR is a disulfide linked heterodimer consisting of an xcex1 and a xcex2 polypeptide which is expressed on the surface of mature T cells. The two chains are similar in size possessing a transmembrane portion encompassed within a constant region and a polymorphic variable region that possesses considerable structural homology with immunoglobulins. Each variable region is composed of a variable (V) segment, a joining (J) segment, and a diversity (D) segment (xcex2 chain only) which assemble into the polymorphic region. Such diversity is necessary for the T cells to respond to a wide variety of antigens.
B cells differentiate in the bone marrow of adult mammals developing from pre-B cells into antibody-producing plasma cells. The importance of B cells to the immune system is highlighted by those rare immunodeficiency diseases in which the patient can only survive by repeated gamma globulin injections. One of the fascinating aspects of B cells is their heterogeneity of antibody expression. It has been estimated from observations that no more than two out of every 108 different antibodies could be identical. Not surprisingly, the mechanisms which are responsible for such diversity are not fully understood. Antibodies and TcRs, both having constant and variable regions, fall into what is referred to as the immunoglobulin superfamily.
The process of immunoglobulin expression is initiated with activation of resting B cells. In the T cell independent pathway, mitogen binds to surface receptors of B cells stimulating expression of fairly low affinity IgM monomers. Upon recognition of foreign antigen, these IgM monomers cross-link at the cell surface and are internalized. Antibody expression then switches to the transcription and translation of higher affinity IgG, IgE, IgA, or pentameric IgM. In the T cell dependent pathway, mitogen is again required to stimulate the resting B cell, however, after internalization, antigen is processed within the cell to reemerge on the cell surface in association with MHC class II molecules. As an antigen presenting cell (APC), antigen-MHC complexes are recognized by and stimulate T cell activation and the production of a number of T and B cell soluble mediators. Information received from these surface complexes is transmitted to the B cell""s nucleus via second messengers which, among other effects, leads to increased cyclic nucleotide metabolism and protein kinase C activity. In both T cell dependent and independent pathways, B cells develop into functionally mature, antibody producing cells.
Antibodies are bifunctional molecules comprising two heavy (H) chains and two light (L) chains joined with interchain disulfide bonds. Each chain contains constant (C) and variable (V) regions, which can be broken down into domains designated CH1, CH2, CH3 and VH, and CL and VL. IgM exists as cell surface monomers or circulating pentamers held together with a 137 amino acid peptide called the J chain. IgA molecules also circulate, but in pairs linked with J chain and contain a small secretory component (SC) which is involved in transport across epithelial membranes. Antibody binds to antigen via the variable region domains contained in the Fab portion and, after binding, interacts with the rest of the immune system through the effector functions of the constant region domain mostly through the Fc portion. Effector functions include activation of the complement cascade, interaction with effector cells such as lymphocytes, and compartmentalization of immunoglobulins. Constant regions are also thought to influence the stabilities of the different immunoglobulins. For example, IgG is relatively stable with a circulating half-life of about 23 days. IgG is also the immunoglobulin responder associated with the secondary immune response. This immunoglobulin fixes complement through the classic complement cascade and has the ability to recruit macrophages and neutrophils. Pentameric IgM is another very strong activator of the classic complement cascade and has a serum half-life of about five days. IgA has a serum half-life of 5-6 days, activates complement through the alternate pathway, and is the principal antibody in mucus secretions.
The antigen binding domains, the variable regions, are encoded in the variable region genes which are somewhat scattered in the genome and must be brought together by a process referred to as somatic recombination. In this process, the V, D and J (not related to the J chain) segments of the host genome are brought together to form a gene region. This region is spliced to the mRNA encoding the antibody""s constant region domain to be expressed together as a polypeptide and ultimately as an antibody molecule.
Antibody constant regions are the principal determining features of antibody class for both heavy and light chains, and are encoded on about fifteen different genes. The five classes of heavy chain genes are designated alpha (xcex1), gamma (xcex3), delta (xcex4), mu (xcexc), and epsilon (xcex5), and the two light chain genes, kappa (xcexa) and lambda (xcex). Variable regions, which contain the antigen binding site, are encoded on upwards of one thousand different genetic regions. These regions selectively recombine to create the amino acid combination required to recognize and bind to the target antigen. Binding site variability is not uniformly distributed, but each domain contains a number of highly variable portions called hypervariable regions (HVR), or complementarity determining regions (CDR), and it is these regions which actually interact with antigen.
The generation of binding-site diversity is a combination of several factors; (1) the combination of different VH and VL domains, (2) the combination of different V, D, and J regions to form the variable domain, (3) the generation of novel diversity at domain junctions referred to as junctional-diversity, and (4) diversity due to somatic mutation. Somatic mutation, to a large extent, is also responsible for maturation of the immune response wherein B cell clones which proliferate during development of the humoral response have an increasingly higher affinity for the antigen. The combination of these processes, in theory, allows an organism to generate a specific immune response to nearly any antigen.
The stimulation of an antibody response is the basis behind most forms of vaccine therapy and prophylaxis. As a prophylaxis, antigen in the form of killed or attenuated microorganism or purified protein is administered to a patient. Administration of this vaccine, it is hoped, will prime the patient""s immune system for the possible later recognition of that same antigen in the form of an infection. If the infection can be caught early, in other words, if anti-antigen antibodies are circulating throughout the body upon initial or early exposure to the organism, the organism may be eliminated from the body before having a chance to take hold or produce a full-blown infection. This aspect has been recognized for a very long time, even before the basic structure of the antibody was appreciated. Antibody treatments involve passive vaccinations of pooled serum in the form of gamma globulin. Blood plasma is collected from convalescent individuals or animals, who recovered from the particular disease, and refined into the proteinaceous or gamma globulin fraction, so named because it contains predominantly IgG molecules. Injections of this gamma globulin are administered many times over a period of hours or days, usually immediately after exposure to the infectious organism or toxic substance, to provide the patient with short-term protection from the infection. For example, individuals bitten by an animal suspected of harboring the rabies virus, a rhabdovirus, are administered a regiment of gamma globulin treatments to prevent the virus from infecting because once an infection takes hold the outcome is inevitably quite poor. However, if treatments are begun early the prognosis can be fairly optimistic.
The use of antibodies for cancer therapy (or prophylaxis) is based on the premise that the antigenic profile of a cancer cell is different from that of normal cells. As depicted schematically in FIG. 1, these differences could potentially include (1) antigenic determinants that are present exclusively on the surface of tumor cells, (2) intracellular molecules found exclusively in tumor cells that are presented as peptides on the cell surface in association with MHC molecules, (3) antigens that are present only on some normal cells, and (4) quantitative differences in the amount of expression of certain antigens on the surface of the tumor cells when compared with other non-tumor cell types. This premise has been substantiated by the discovery of socalled tumor-associated antigens which are not expressed in significant or measurable amounts on the surfaces of normal cells (M. Herlyn and H. Koprowski, Ann. Rev. Immunol. 6:283-308, 1988). These tumor-specific peptides are presented on the cell surface in association with class I MHC antigens.
Monoclonal antibodies, unlike polyclonal antibodies, comprise a collection of identical molecules produced by a common B cell clone which are directed against a single antigenic determinant. Monoclonal antibodies can be distinguished from polyclonal antibodies in that monoclonal antibodies must be individually selected whereas polyclonal antibodies are selected in groups of more than one or, in other words, in bulk. Large amounts of monoclonal antibodies can be produced by immoitalization of a polyclonal B cell population using hybridoma technology. Each immortalized B cell can divide, presumably indefinitely, and gives rise to a clonal population of cells that each expresses an identical antibody molecule. The individual immortalized B cell clones, the hybridomas, are segregated and cultured separately.
Monoclonal antibody therapy has been increasingly used in cancer therapy and diagnosis, but suffers from several limitations. (H. Thomas and K. Sikora, Rev. Oncol. 4:107-120, 1991). Tumor cell variants, lacking the single antigenic determinant recognized by the monoclonal antibody often arise which escape treatment. Because each monoclonal antibody is directed to a single antigenic determinant on the targeted cancer cell, the density of that determinant on the cell surface is usually not high enough to allow for destruction of the cell. Further, the effector mechanisms mediated by the Fc regions of the bound antibody molecules, such as complement binding and concomitant production of C3b, opsonization/phagocytosis, and antibody-dependent, cell-mediated cytotoxicity (ADCC), are not activated. Only at high antibody densities is complement activated, or enough Fc receptors engaged, so that effector cells are triggered to perform their preordained functions. Consequently, anti-tumor monoclonal antibodies are usually ineffective for complete elimination of the target cells.
In an effort to circumvent some of these problems, methods have been developed to try and bolster the killing efficiency of monoclonal antibodies with radioactive isotopes, toxins or drugs. However, these tags can in turn cause deleterious side effects (T. A. Waldmann, Sci. 252:1657-62, 1991). Even if a monoclonal antibody (tagged or untagged) is reasonably effective at eliminating cancer cells, and remissions have been documented, in most cases the cancer relapses because tumor cell variants which have lost the target antigenic determinant escape and proliferate (R. A. Miller et al., N. Engl. J. Med. 306:517-22, 1982). This problem might be partially overcome with the use of collections of anti-tumor monoclonal antibodies which would have the benefit of using the same preexisting reagent on many patients. Although this would be a advantage, because individual tumors are so variable, the finding of multiple antigens specific to one cancer type present on all cancers of that type is not expected to be a common occurrence (D. Berd et al., Cancer Res. 49:6840-44, 1989). Even if an effective treatment using collections of monoclonal antibodies is found for patients with some types of cancer, it is unlikely to be an effective treatment for many forms of neoplasia.
Monoclonal antibody technology, in its present stage, has focused on the use of non-human monoclonal antibodies. This often presents a problem because patients develop antibodies to the non-human regions of the proteins including both the constant and variable regions. Antibodies reactive against the antigen binding site, the variable regions, of another antibody are called anti-idiotypic antibodies. Murine monoclonal antibodies, the easiest to produce and most prevalent, have been shown to induce a humoral response in humans which is referred to as the human anti-mouse antibody response or the HAMA response (D. L. Sawler et al., J. Immunol. 135:1530-35, 1985). Significant HAMA responses in patients receiving such therapy, besides destroying any possible benefit of the treatment, introduces numerous complications including immune complex disorders.
In recent years, these problems have been partially solved by the generation and use of chimeric antibodies. Chimeric antibodies have V regions derived from the tumor-specific mouse monoclonal antibody, but human C regions (S. L. Morrison and V. T. Oi, Adv. Immunol. 44:65-92, 1989). In such forms, the HAMA response is significantly reduced (although not eliminated), but there is still the anti-idiotypic response to deal with. Efforts to eliminate the anti-idiotypic response have involved the engineering of antibodies in which only the CDRs are derived from the mouse antibody and the framework and C regions are of human origin. These are the so-called humanized antibodies (P. C. Caron et al., Cancer Res. 52:6761-67, 1992). These antibodies are very difficult to create involving multiple cloning events and may still elicit anti-idiotypic antibodies (ibe Third Annual IBC International Conference on Antibody Engineering, Dec. 14-16, 1992, San Diego). Completely humanmonoclonal antibodies are presently being developed, with the hope that they will not elicit anti-idiotypic antibodies (C. J. Fisher et al., Critical Care Med. 18:1311-15, 1990). However, as mice are perfectly capable of generating anti-idiotypic antibodies to antibodies derived from the same species and even from the same inbred strain, the generation of anti-idiotypic antibodies after the injection of large amounts of antibodies with identical V regions will remain a problem as long as monoclonal antibodies are used.
The use of polyclonal antibodies would overcome some of the drawbacks associated with monoclonal antibody therapy. Unlike monoclonal antibodies, polyclonal antibodies are directed to many different antigenic determinants on the target cell surface and would bind with sufficient density to allow the effector mechanisms of the immune system to work efficiently possibly eliminating any need for radioactive or toxic tags. Furthermore, the chance that tumor cell escape variants which have lost reactivity with all of the polyclonal antibodies would arise is exceedingly small. Anti-idiotypic reactivity in patients is not expected to be a problem because no one V region combination should be present in sufficient quantity to elicit a significant response.
There are several problems associated with the use of conventional polyclonal antibodies. First, polyclonal antibodies in the form of gamma globulin, is available in a very limited supply, insufficient for widespread human treatments. Second, when used on apatient, many of the polyclonal antibodies will be absorbed by the patient""s normal cells and tissues. The number of different antibodies which remain after absorption would be exceedingly small, possibly too small to be of any beneficial effect. Thirdly, this supply, besides being inadequate, requires a great deal of purification to remove unwanted materials, such as cytokines and other immunoregulatory proteins, which may elicit undesirable immune responses and side effects. There is also a substantial risk of contamination associated with infectious organisms such as HIV or toxins such as lipopolysaccharide, which may be present in the source. These problems are difficult to overcome because of composition variability as the material is collected from many different biological sources. Recombinant production of polyclonal antibodies would address certain of these issues, but the genes encoding these antibodies are not readily identifiable and the technology to efficiently work with collections of antibody genes has yet to be developed.
Recently, antigen-binding antibody fragments have been expressed on the surface of filamentous phage (G. P. Smith, Sci. 228:1315, 1985). Libraries of H and L variable region cDNAs have been obtained from animal and human B cells and cloned in pairs in random H-L combinations into phage display vectors to produce combinatorial libraries displaying Fab or single-chain Fv fragments (W. D. Huse et al., Sci. 246:1275-81, 1989). Fab is formed by the association of L chain with the VH and CH1 domains of the H chain, the Fd region. In phage display libraries, the carboxyl-terminal end of the Fd or Fv region is tethered to a fragment of a phage coat protein, such as cpIII or cpVIII, which anchors the Fab fragment to the surface of the phage. In both Fab and Fv fragments, as in the intact antibodies, the antigen-binding site is formed from the combination of the VH and VL domains.
Phage display libraries can be selected for binding to specific antigens by affinity chromatography (R. E. Hawkins et al., J. Mol. Biol. 226:889, 1992) or by panning phage on antigen-coated surfaces (C. F. Barbas et al., Proc. Natl. Acad. Sci. USA 88:4363, 1991). As the DNA segments encoding the selected antibody fragments are carried by phage particles, the selected phage particles encoding monoclonal antibody fragments can be isolated and propagated indefinitely. The selected phage clones can be modified to produce antibody fragments devoid of the coat protein moiety that may also be secreted from the bacterial cells. Antibody fragments specific for haptens, proteins and several human viruses have been recovered from such phage display combinatorial libraries (J. D. Marks et al., J. Mol. Biol. 222:581, 1991; R. A. Williamson et al., Proc. Natl. Acad. Sci. USA 90:4141, 1993).
One major drawback of these combinatorial libraries is that the VH and VL regions which form the antigen binding domain are randomly associated. The original combinations of H and L chains that were so efficiently selected in vivo by the antigen are lost (J. McCafferty et al., Nature 348:552-54, 1990). The chance of finding H and L combinations with high affinity for the antigen of interest is very small. The number of clones that would need to be screened for the presence of specific binding to the antigen is increased by orders of magnitude.
A method for amplifying and linking the expressed VH and VL region genes within single cells in a population of cells has been very recently reported (M. J. Embleton et al., Nuc. Acids Res. 20:3831-37, 1992). This method was exemplified with two mouse hybridoma cell lines, each producing a known and distinct immunoglobulin (Ig) product. The two cell populations were mixed, fixed with formaldehyde and permeabilized with the detergent NP-40. cDNAs were synthesized using reverse transcriptase and primers complementary to the 3xe2x80x2 ends of the VH and VL mRNAs. The cDNAs were then amplified by PCR and linked in the same reaction using, in addition to the cDNA primers, one primer from the 3xe2x80x2 end of the VH gene and one primer from the 5xe2x80x2 end of the VL gene. These primers also contained complementary tails of extra sequence for the self-assembly of the VH and VL genes. In a second PCR, after washing the cells, the linked VH and VL region genes were amplified with terminal nested primers yielding a population of DNA fragments which encoded the VH and VL sequences in a head-to-tail transcriptional orientation. These DNA fragments were recovered from the cell supernatants.
Although this report claimed that almost all VH-VL combinations examined were derived from only one of the hybridoma cell lines, the method results in mixed VH-VL combinations wherein VH and VL can be derived from different cells. That VH-VL mixing should occur is also apparent from theoretical considerations. As the linked VH-VL combinations are recovered from the supernatant of the fixed/permeabilized cells, the pores in the membranes of these cells allow free passage of such linked DNA molecules, one would expect that the smaller VH and VL DNA molecules could exit the cells and become linked and be further amplified outside the cells where free mixing of VH and VL from different cells would occur.
The present invention overcomes the problems and disadvantages associated with current strategies and designs and provides new compositions and methods for the prophylaxis and treatment of certain diseases and disorders.
Polyclonal antibody libraries have a higher complexity than monoclonal antibodies or antibody cocktails, being directed against many different antigenic determinants and carry the option to use radioactive, toxin, and other tags for both therapy and diagnosis. One embodiment of the invention is directed to methods for treating neoplastic disorders using polyclonal antibody libraries specifically directed to a disease or disorder. A sample of neoplastic tissue is obtained from a patient. The sample is introduced to a cell population capable of producing antibodies such as the spleen cells of a mammal. The cell population is fixed, permeabilized and the VH and VL mRNA molecules reverse transcribed into VH and VL cDNA sequences. The cDNA sequences are PCR amplified and the amplified sequences linked, preferably in a head-to-head transcriptional orientation. The linked sequences are again PCR amplified to create a population of DNA fragments which encode the VH and VL antibody regions. These DNA fragments are cloned into expression vectors and the different populations of expression vectors expanded in the transfected host. Expression vectors which encode a library of recombinant anti-neoplastic antibodies are selected and the subpopulations or sublibraries expanded again. The recombinant anti-neoplastic antibodies produced by these vectors are then administered to the patient. The neoplastic disorders which can be treated include leukemias, lymphomas, sarcomas, carcinomas, neural cell tumors, squamous cell carcinomas, germ cell tumors, metastases, undifferentiated tumors, seminomas, melanomas, neuroblastomas, mixed cell tumors, neoplasias caused by infectious agents and other malignancies.
Another embodiment of the invention is directed to the in vivo diagnosis of a neoplastic disorder by imaging the diseased tissue in a patient. A library of patient-specific, anti-neoplastic antibodies are created, as described herein, and labeled with a detectable label. The antibodies may be whole or fragments of antibodies such as Fab fragments. The labeled library is administered to the patient and the label detected using, for example, radioactive detectors, visual inspection, nuclear magnetic resonance (NMR) detection, or other means to detect the appearance of label in a bodily tissue or waste, or within the whole body itself. From these methods, heretofore unidentified neoplasias may be perceived which escaped detection by other means. Also, once detected the neoplasia can be effectively monitored during treatment regiments.
Another embodiment of the invention is directed to methods for creating patient-specific or antigen-specific libraries of polyclonal antibodies. These libraries, created as described above, are useful for the treatment or prophylaxis of a number of diseases including neoplasia, malignancies, infections, genetics defects and genetic deficiencies. Libraries may comprise vectors containing DNA encoding the variable regions, DNA encoding the entire antibody, or antibodies or antibody fragments. Once isolated and cloned, the library can be expanded to ensure the representation of every member of the antigenic profile and can also be easily transferred to other vectors.
Another embodiment of the invention is directed to compositions containing libraries of polyclonal antibodies or genetic expression vectors which encode these antibodies. The library or selected sub-library of antibodies may be labeled with a detectable label and/or contain a pharmaceutically acceptable carrier. Compositions can be administered to patients for diagnostic or treatment protocols. Alternatively, libraries of vectors may be administered to patients for the in vivo expression of antibodies or antibody fragments.
Another embodiment of the invention is directed to diagnostic aids or kits and methods for using these kits for the detection of diseases and disorders. Diagnostic aids or kits comprise a polyclonal antibody library which may be labeled with a detectable label to which is added a sample suspected of containing tharet antigen. The sample may be a sample of bodily fluid such as blood, serum, plasma, spinal fluid, lymph or urine. The presence of absence of the target antigen indicates the presence of a particular disease, disorder or contaminant. Samples may be biological samples from a patient or biological samples from an environmental source suspected of harboring a contaminant. Sample is mixed with the library and the presence of antigen confirmed by the binding of a significant number of antibodies and detection of the label.
Another embodiment of the invention is directed to methods for creating and utilizing libraries of receptor proteins which possess variable regions. Receptor proteins which may be utilized to create a library include T-cell receptors, B-cell receptors, natural killer cell receptors and macrophage receptors. A sample of biological tissue is introduced to a cell population capable of producing receptor proteins. Variable region receptor protein mRNAs are reverse transcribed into cDNA sequences which are PCR amplified and the resulting DNA fragments cloned into expression vectors. The expression vectors which encode the recombinant receptor proteins are selected and a subpopulation selected expanded to produce the library. These libraries can be used to diagnose, image or treat diseases and disorders including neoplasias, infections and genetic defects and deficiencies. In addition, using these same methods libraries of chimeric proteins containing both antibody and receptor protein portions may also be created and utilized.
Another embodiment of the invention is directed to nucleic acid vectors which can be used to create the antigen-specific polyclonal antibody libraries. These vectors comprise restriction enzyme recognition sites convenient for the cloning of nucleic acid fragments and sequences to efficiently PCR amplify the cDNA fragments. The vectors are designed to have one or more pairs of genetic fragments inserted in a head-to-head transcriptional orientation and, optionally, further comprise transcription and translation controlling sequences such as TATA boxes, CAT boxes, ribosome binding sites, RNA polymerase initiation and termination sites, leader sequences, strong transcriptional promoters which may be differentially regulated or parts or combinations thereof.
Another embodiment of the invention is directed to methods for transferring a library of nucleic acid fragments between different vectors without significant loss of library diversity. The library of fragments is inserted into first vectors in a head-to-head transcriptional orientation to form recombinant vectors. The inserts of these recombinant vectors are transferred into second vectors by, for example, PCR amplification of the inserted sequences or restriction enzyme cloning, and the fragments reinserted into second vectors without significant loss of library diversity.
Other embodiments and advantages of the invention are set forth, in part, in the description which follows and, in part, will be obvious from this description or may be learned from the practice of the invention.